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High-Throughput Sequencing Techniques for the Detection and Survey of Marine Non-Indigenous Species : a Valuable Addition to Traditional Methods ? Marjorie Couton

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High-throughput sequencing techniques for the detection and survey of marine non-indigenous species : a valuable addition to traditional methods ? Marjorie Couton To cite this version: Marjorie Couton. High-throughput sequencing techniques for the detection and survey of marine non- indigenous species : a valuable addition to traditional methods ?. Ecosystems. Sorbonne Université, 2020. English. NNT : 2020SORUS039. tel-03180937 HAL Id: tel-03180937 https://tel.archives-ouvertes.fr/tel-03180937 Submitted on 25 Mar 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Sorbonne Université Ecole doctorale 227 Sciences de la nature et de l’Homme : évolution et écologie UMR7144 Adaptation et Diversité en Milieu Marin Equipe Dynamique de la Diversité marine High-throughput sequencing techniques for the detection and survey of marine non-indigenous species: a valuable addition to traditional methods? Le séquençage haut-débit pour détecter et étudier les espèces marines non- indigènes : un complément pertinent aux méthodes traditionnelles ? Par Marjorie Couton Thèse de doctorat en Ecologie Marine Sous la direction de Frédérique Viard et Thierry Comtet Présentée et soutenue publiquement le 29 octobre 2020 Devant un jury composé de : Pr TURON Xavier, Professeur, Centre d’études avancées de Blanes Rapporteur Dr RODRIGUEZ-EZPELETA Naiara, Directrice de recherche, AZTI Rapporteure Dr NUNES Flavia, Directrice de recherche, Ifremer Examinatrice Pr DESTOMBES Christophe, Professeur, Sorbonne Université Examinateur Dr VIARD Frédérique, Directrice de recherche, CNRS Directrice de thèse Dr COMTET Thierry, Chargé de recherche, CNRS Co-directeur de thèse Remerciements En tout premier lieu, j’aimerais remercier mes superviseurs, Frédérique Viard et Thierry Comtet pour leur soutien et leurs encouragements. Toutes nos discussions, formelles et informelles, ainsi que leurs conseils et remarques avisés, m’ont permis de ne pas me reposer sur mes acquis et de toujours me remettre en question. Tous les progrès réalisés et la maturité acquise lors de ces trois dernières années n’auraient pas été possibles sans vous. Bien plus qu’un support scientifique, vous m’avez permis de réaliser cette thèse dans une ambiance bienveillante et amicale, ce qui représente, à mon sens, la majeure partie d’un travail réussi. Contrairement à ce qui pourrait transparaitre au travers d’un manuscrit, une thèse est une aventure collective et aucun des résultats décrits ici n’auraient pu être acquis sans l’aide d’un grand nombre de personnes. C’est le cas de Claire qui m’a épaulé tout au long de ce périple, de l’échantillonnage jusqu’au séquençage. Ses compétences et son expérience au laboratoire m’ont évité pas mal de faux pas. C’est également le cas de Laurent qui a réalisé toutes les identifications morphologiques présentées et dont l’expérience du terrain a été d’une aide précieuse. Enfin Erwan m’a également accordé de son temps pour jeter un œil avisé de bioinformaticien sur mes travaux et me conseiller dans mes analyses. A vous trois un, grand merci. J’aimerais également rendre hommage à tous ceux qui m’ont aidée pour les échantillonnages. Merci aux plongeurs, Mathieu, Wilfried et Yann, pour leur indéfectible bonne humeur, merci aux marins, François, Gilles et Noël pour leur gentillesse, malgré des conditions parfois difficiles, et merci également à Stéphane et Jérôme pour patience et leur efficacité. Je suis aussi reconnaissante envers Marion et Aurélien pour leur aide au laboratoire, envers l’équipe du CRBM et notamment Gaëtan pour la mise en place de matériel pour la remontée des panels de recrutement, ainsi qu’à la plateforme Genomer, et surtout Gwenn et Erwan, pour leur aide lors des séquençages. Enfin, parce que les interactions sociales sont très importantes pour un travail efficace (cf. le confinement), je tiens à remercier tous ceux avec qui j’ai pu passer des moments de discussions informelles et de détente pendant ces trois ans. Merci à toute l’équipe ABiMS pour leur accueil chaleureux, leurs pauses café/gâteaux de 10h30, les blagues du mercredi et surtout pour ne pas m’avoir retiré de l’alias igm3 pour que je puisse continuer à venir m’incruster de temps en temps après avoir déménagé dans un autre bâtiment. Merci à Delphine pour nos randonnées, parfois un peu plus longues que prévues à cause de notre mauvais sens de l’orientation, merci à Anaëlle et Anaïs pour les discussions autour d’un café et pour m’avoir supportée (dans les deux sens du terme) lors de la dernière ligne droite, et merci à Romain pour nos balades quotidiennes qui m’ont permis de me changer un peu les idées pendant la rédaction de ce manuscrit. Et parce que travailler pendant le confinement n’a pas été une mince affaire, merci à mes sœurs, Gaëlle et Solène, pour m’avoir permis de conserver ma santé mentale pendant ces deux mois compliqués. Et pour tous ceux que j’ai pu oubliés et qui ont participé, de près ou de loin, à la création de ce travail, MERCI ! Table of contents Introduction 1 1. Biological invasions: one facet of the global change …………………….……………………..3 a. Biological introductions – definition and global overview ..………..…….………………………..…..3 b. A dynamic process (from introduction to invasion, and failure) .……….………………….…..……5 c. Consequences and management of biological invasions ..……………………………..…………..….7 2. Some important properties of marine biological introductions ………….………………..10 a. Introduction vectors responsible for specific patterns and processes ……………….………...10 b. Marinas and ports as invasion hubs ………………..…………………………………….……….…………….13 3. Molecular tools for the biomonitoring of non-indigenous species ………………………16 a. A furnished DNA-based toolbox with many applications …………………..……………….……….17 b. NIS identification through DNA barcoding: general principle .……..………………….…………..20 c. Producing and processing metabarcoding data .………………………..………………….…………….22 Thesis objectives .…………………………………………………...………………..………………………………..32 Chapter I : High-Throughput Sequencing on preservative ethanol is effective at jointly examining infra-specific and taxonomic diversity, although bioinformatics pipelines do not perform equally 37 Preamble ……………………………………………………………………………………………………………..……39 Abstract …………………………………………………………………………………………………………………….41 Introduction ……………………………………………………………………………………………………………...42 Materials and methods ………………….…………………………………………………………………………..43 a. Case study & sampling …………..……………………………………………..………………………………...……43 b. Sanger sequencing on individual zooid (SSIZ) ………………………..………..…………………………..45 c. High-throughput sequencing on assemblages (HTSA) ……………………..……..………………..…45 Sample processing ……………………………………………………….................…………………...……45 Reads processing …………………………………………..………………………….………………………...47 d. Data analyses ……………………………………..…………………………………………………………………………48 Assignment ………………………………………………………………………………………………………....48 Haplotype comparison ………………………………………………………………………………….…….48 Diversity indices ……………………………………………………………………………………………..……48 Results ……………………………………………………………………………………………………………………….49 a. Sanger sequencing on individual zooid (SSIZ) ...…………………………………………………………...49 b. Species assignment ………………………………………………………………………………………………………49 c. Pipeline performance for HTSA-based haplotype detection ………………………………………..50 d. Population diversity indices ………………………………………………………………………………………….54 Discussion ………………………………………………………………………………………………………………….55 a. Ethanol-based DNA is a valid non-destructive alternative to bulkDNA, even after several months of storage ………………………………………………………………………………………..…..55 b. Specific primers can improve the quantitative use of HTSA data …………………………………56 c. Careful choice of bioinformatics pipeline is needed to examine genetic diversity ………57 d. Improving haplotype detection – a matter of compromise ………………………………………….58 References …………………………………………………………………………………………………………………60 Chapter II : How effective is metabarcoding for studying communities living in marinas? 65 Preamble ………………………………………………………………………………………………….……………….67 Chapter II.1: Non-indigenous and native species from biofouling communities in marinas: the (un)detected fraction from environmental DNA metabarcoding ..........…67 Abstract ………………………………………………………………………………………………..……………………69 Introduction ……………………………..………………………………………………………………………………..69 Materials and methods ………………………………..…………………………………………………………….71 a. Sampling …………………………………………………………………………………………………..…………………..71 b. DNA extraction …………………………………………………………………………………………..…………………73 c. Library preparation and sequencing …………………………………………………………..………………...74 d. Reads processing and filtering ……………………………………………………………………..………………76 e. Taxonomic assignment ………………………………………………………………………………..……………….76 f. Comparison between quadrats and metabarcoding datasets ………………….………..………...77 Results .………………………………………………………………………………………………………………………78 a. Reads processing and taxonomic assignment …………………………………………….……………….78 b. Comparison of quadrats (morphology-based) and eDNA metabarcoding datasets .…..80 c. Effect of the sampling strategy on taxa detection ……………………………………………….……….84 Discussion .…………………………………………………………………………………………………………………86
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    Anuário do Instituto de Geociências - UFRJ www.anuario.igeo.ufrj.br As Famílias Veneridae, Trochidae, Akeridae e Acteonidae (Mollusca), na Formação Romualdo: Aspectos Paleoecológicos e Paleobiogeográicos no Cretáceo Inferior da Bacia do Araripe, NE do Brasil The Families Veneridae, Trochidae, Akeridae and Acteonidae (Mollusca), in the Romualdo Formation: Paleoecological and Paleobiogeographic Aspects in the Lower Cretaceous of the Araripe Basin, NE of Brazil Priscilla Albuquerque Pereira1; Rita de Cassia Tardin Cassab2 & Alcina Magnólia Franca Barreto1 1Universidade Federal de Pernambuco, Centro de Tecnologia e Geociências, Departamento de Geologia, Laboratório de Paleontologia, Av. Hélio Acadêmico Ramos, s/n, Cidade Universitária, 50740-533, Recife, PE, Brasil 2 Universidade Federal do Rio de Janeiro, Instituto de Geociências, Departamento de Geologia, Avenida Athos da Silveira Ramos, 274, 21910-900, Cidade Universitária, Ilha do Fundão, s/n, Rio de Janeiro, Rio de Janeiro-RJ, Brasil E-mail: [email protected]; [email protected]; [email protected] Recebido em: 18/07/2018 Aprovado em: 21/09/2018 DOI: http://dx.doi.org/10.11137/2018_3_137_152 Resumo Moluscos fósseis na Bacia Sedimentar do Araripe são relatados desde a década de 1960, com biválvios presentes nas forma- ções Crato, Romualdo e gastrópodos, restritos a Formação Romualdo. A identiicação e descrição desses moluscos tem auxiliado na reconstituição paleoambiental da Formação Romualdo (Aptiano-Albiano) e na interpretação da rota de incursão marinha que aponta para inluência do mar de Tétis na bacia. Este trabalho, descreve e ilustra fósseis coletados nas localidades de Zé Gomes, Cedro/ Tabuleiro e Santo Antônio município de Exu, Pernambuco, pontuando a paleoecologia e a distribuição paleogeográica dos gêneros, além de observar as ainidades faunísticas entre as formaçõe Romualdo e Riachuelo.
  • General Background

    General Background

    Guidelines for the Establishment of Environmental Quality Objectives and Targets in the Coastal Zone of the Western Indian Ocean (WIO) Region October 2009 WIO region: Environmental Quality Objectives and Targets October 2009 First published in Kenya in 2009 by the United Nations Environment Programme (UNEP)/Nairobi Convention Secretariat and the Council for Scientific and Industrial Research of South Africa (CSIR). Copyright © 2009, UNEP/Nairobi Convention Secretariat and CSIR. UNEP/GEF WIO-LaB Technical Report Series No. 2009/7 CSIR Report Number: CSIR/NRE/CO/ER/2009/0115/A Copyright notice: This publication may be reproduced in whole or in part and in any form for educational or non-profit purposes without special permission from the copyright holder provided that acknowledgement of the source is made. UNEP/Nairobi Convention Secretariat and CSIR would appreciate receiving a copy of any publication that uses this publication as a source. No use of this publication may be made for resale or for any other commercial purpose without prior permission in writing from UNEP/Nairobi Convention Secretariat and CSIR. Disclaimer: The contents of this report do not necessarily reflect the views and policies of UNEP. The designations employed and the presentations do not imply of any opinion whatsoever on the part of the UNEP, or of any cooperating organization concerning the legal status of any country, territory, city or area, of its authorities, or of the delineation of its territories or boundaries. For additional information please contact: UNEP/Nairobi Convention Secretariat Council for Scientific and Industrial Research (CSIR) United Nations Environment Programme P O Box 17001, Durban, South Africa United Nations Avenue, Gigiri, Tel: +27 31 2422356 P.O Box 47074, Nairobi, Kenya Fax: +27 31 2612509 Tel: +254 20 7621250/7622025 E-mail: [email protected] E-mail: [email protected] Principal Authors: Susan Taljaard (CSIR, Stellenbosch), Steven Weerts (CSIR, Durban), Shamilla Pillay (CSIR, Durban) and Anisha Rajkumar (CSIR, Durban) Technical Editors: Dr.
  • From Western Samoa

    From Western Samoa

    E . Schwabe 1 & F. J . A . S l i e ker 2 1Zoologische Staatssammlung München 2N a t u u r museum Rotterd a m A new species of C a l l o c h i t o n G r ay, 1847 (Mollusca: Po lyplacophora) from Western Samoa Schwabe, E. & Slieker, F.J.A., 2001 - A new species of C a l l o c h i t o n G r a y, 1847 (Mollusca: Polyplacophora) from Western Samoa - DEINSEA 8: 225-228 [ISSN 0923-9308]. Published 09 November 2001 Among molluscan material from Western Samoa collected by H. Bayer and sent to the first author an unknown species of chiton was found. It is here described as Callochiton mumuena spec. nov. The new taxon is only known from the holotype, collected on Savaii Island under coral slab at a depth of one metre. Keywords: Mollusca, Polyplacophora, Callochiton, new species, Western Samoa Correspondence: Enrico Schwabe, Zoologische Staatssammlung München, Münchhausenstraße 21, 81247 München, Germany, e-mail [email protected]; Frans J. A. Slieker, Natuurmuseum Rotterdam, P.O. Box 23452, 3001 KL Rotterdam, T h e Netherlands, e-mail natuurmuseum@nmr. n l I N T RO D U C T I O N M ATERIAL EXAMINED R e c e n t l y, Mr H. Bayer (Savaii Island, For direct comparison the following material Western Samoa) has sent many molluscan was studied: Callochiton empleurus (HU T TO N, specimens to the first author. This material 1872) from New Zealand (National Museum included several different chiton species, of of New Zealand, Wellington: lectotype which the following could be identified: NMNZ M279); Callochiton klemi AS H B Y, To n i c i a (L u c i l